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Congratulations on the new Kindle.
If you're just looking for opinions... I keep all my books in Calibre. I only keep 15-20 books on my Kindle at a time. I can't read that many books at once anyway! It's no problem for me to connect to my computer to load a new book any time I want.
I've also heard the Kindle takes a very long time to index your collection if you put a few thousand books on it. (Can't imagine why people would want or need that many books on the Kindle at once)
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